* Package:    sci-chemistry/gromacs-2021.3-r1
 * Repository: gentoo
 * Maintainer: alexxy@gentoo.org sci-chemistry@gentoo.org
 * USE:        abi_x86_64 amd64 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 custom-cflags doc double-precision elibc_musl fftw gmxapi gmxapi-legacy hwloc kernel_linux lmfit offensive openmp python_single_target_python3_9 single-precision threads tng userland_GNU
 * FEATURES:   network-sandbox preserve-libs sandbox userpriv usersandbox
 * Using python3.9 to build
>>> Unpacking source...
>>> Unpacking gromacs-2021.3.tar.gz to /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work
>>> Unpacking manual-2021.3.pdf to /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work
unpack manual-2021.3.pdf: file format not recognized. Ignoring.
>>> Source unpacked in /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work
>>> Preparing source in /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3 ...
 * Source directory (CMAKE_USE_DIR): "/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3"
 * Build directory  (BUILD_DIR):     "/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3_build"
 * Hardcoded definition(s) removed in CMakeLists.txt:
 *      set(CMAKE_INSTALL_PREFIX "/usr/local/gromacs" CACHE STRING "Installation 
 *      set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose the type of build, op
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3 ...
 * Configuring for float precision
 * Source directory (CMAKE_USE_DIR): "/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3"
 * Build directory  (BUILD_DIR):     "/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3_float"
cmake -C /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3_float/gentoo_common_config.cmake -G Ninja -DCMAKE_INSTALL_PREFIX=/usr -DGMX_FFT_LIBRARY=fftw3 -DGMX_USE_LMFIT=EXTERNAL -DGMX_X11=no -DGMX_EXTERNAL_BLAS=no -DGMX_EXTERNAL_LAPACK=no -DGMX_OPENMP=yes -DGMX_COOL_QUOTES=yes -DGMX_USE_TNG=yes -DGMX_BUILD_MANUAL=no -DGMX_HWLOC=yes -DGMX_DEFAULT_SUFFIX=off -DGMX_SIMD=AVX2_256 -DGMX_VMD_PLUGIN_PATH=/usr/lib/vmd/plugins/*/molfile/ -DBUILD_TESTING=no -DGMX_BUILD_UNITTESTS=no -DPYTHON_EXECUTABLE=/usr/bin/python3.9 -DGMX_DOUBLE=OFF -DGMX_MPI=OFF -DGMX_THREAD_MPI=yes -DGMXAPI=yes -DGMX_INSTALL_LEGACY_API=yes -DGMX_GPU=OFF  -DGMX_BINARY_SUFFIX= -DGMX_LIBS_SUFFIX= -DGMX_PYTHON_PACKAGE=no -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCMAKE_TOOLCHAIN_FILE=/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3_float/gentoo_toolchain.cmake  /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3
loading initial cache file /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3_float/gentoo_common_config.cmake
-- The C compiler identification is GNU 11.2.0
-- The CXX compiler identification is GNU 11.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/x86_64-gentoo-linux-musl-gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/x86_64-gentoo-linux-musl-g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found Python3: /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/temp/python3.9/bin/python3 (found suitable version "3.9.9", minimum required is "3.6") found components: Interpreter 
-- Found OpenMP_C: -fopenmp (found version "4.5") 
-- Found OpenMP_CXX: -fopenmp (found version "4.5") 
-- Found OpenMP: TRUE (found version "4.5")  
-- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS
-- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS
-- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - not found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - not found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - found
-- Using manually set binary suffix: ""
-- Using manually set library suffix: ""
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version: 
-- Found HWLOC: /usr/lib/libhwloc.so (found suitable version "2.5.0", minimum required is "1.5") 
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE  
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Performing Test TEST_ATOMICS
-- Performing Test TEST_ATOMICS - Success
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - supported
-- Detected build CPU vendor - AMD
-- Detected build CPU brand - AMD Ryzen 9 5950X 16-Core Processor
-- Detected build CPU family - 25
-- Detected build CPU model - 33
-- Detected build CPU stepping - 0
-- Detected build CPU features - aes amd apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf misalignsse mmx msr nonstop_tsc pclmuldq pdpe1gb popcnt pse rdrnd rdtscp sha sse2 sse3 sse4a sse4.1 sse4.2 ssse3
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for system XDR support
-- Checking for system XDR support - not present
-- Performing Test C_mavx2_mfma_FLAG_ACCEPTED
-- Performing Test C_mavx2_mfma_FLAG_ACCEPTED - Success
-- Performing Test C_mavx2_mfma_COMPILE_WORKS
-- Performing Test C_mavx2_mfma_COMPILE_WORKS - Success
-- Performing Test CXX_mavx2_mfma_FLAG_ACCEPTED
-- Performing Test CXX_mavx2_mfma_FLAG_ACCEPTED - Success
-- Performing Test CXX_mavx2_mfma_COMPILE_WORKS
-- Performing Test CXX_mavx2_mfma_COMPILE_WORKS - Success
-- Enabling 256-bit AVX2 SIMD instructions using CXX flags:  -mavx2 -mfma
-- Detecting flags to enable runtime detection of AVX-512 units on newer CPUs
-- Performing Test C_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED
-- Performing Test C_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED - Failed
-- Performing Test C_xCORE_AVX512_FLAG_ACCEPTED
-- Performing Test C_xCORE_AVX512_FLAG_ACCEPTED - Failed
-- Performing Test C_mavx512f_mfma_FLAG_ACCEPTED
-- Performing Test C_mavx512f_mfma_FLAG_ACCEPTED - Success
-- Performing Test C_mavx512f_mfma_COMPILE_WORKS
-- Performing Test C_mavx512f_mfma_COMPILE_WORKS - Success
-- Performing Test CXX_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED
-- Performing Test CXX_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED - Failed
-- Performing Test CXX_xCORE_AVX512_FLAG_ACCEPTED
-- Performing Test CXX_xCORE_AVX512_FLAG_ACCEPTED - Failed
-- Performing Test CXX_mavx512f_mfma_FLAG_ACCEPTED
-- Performing Test CXX_mavx512f_mfma_FLAG_ACCEPTED - Success
-- Performing Test CXX_mavx512f_mfma_COMPILE_WORKS
-- Performing Test CXX_mavx512f_mfma_COMPILE_WORKS - Success
-- Detecting flags to enable runtime detection of AVX-512 units on newer CPUs -  -mavx512f -mfma
-- Performing Test _Wno_unused_command_line_argument_FLAG_ACCEPTED
-- Performing Test _Wno_unused_command_line_argument_FLAG_ACCEPTED - Success
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_ 
-- Performing Test _callconv_  - Success
-- Checking for module 'fftw3f'
--   Found fftw3f, version 3.3.10
-- Looking for fftwf_plan_many_dft in /usr/lib/libfftw3f.so
-- Looking for fftwf_plan_many_dft in /usr/lib/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/libfftw3f.so
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/libfftw3f.so
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/libfftw3f.so - found
-- Looking for fftwf_have_simd_sse in /usr/lib/libfftw3f.so
-- Looking for fftwf_have_simd_sse in /usr/lib/libfftw3f.so - not found
-- Looking for fftwf_have_sse in /usr/lib/libfftw3f.so
-- Looking for fftwf_have_sse in /usr/lib/libfftw3f.so - not found
-- Looking for fftwf_have_simd_sse2 in /usr/lib/libfftw3f.so
-- Looking for fftwf_have_simd_sse2 in /usr/lib/libfftw3f.so - found
-- Using external FFT library - FFTW3
-- Could not convert sample image, ImageMagick convert can not be used. A possible way to fix it can be found here: https://alexvanderbist.com/2018/fixing-imagick-error-unauthorized
-- Found Sphinx: /usr/bin/sphinx-build (found suitable version "4.2.0", minimum required is "1.6.1") found components: pygments 
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- Performing Test HAS_NO_REDUNDANT_MOVE
-- Performing Test HAS_NO_REDUNDANT_MOVE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_MISSING_DECLARATIONS
-- Performing Test HAS_NO_MISSING_DECLARATIONS - Success
-- Performing Test HAS_NO_NULL_CONVERSIONS
-- Performing Test HAS_NO_NULL_CONVERSIONS - Success
-- Performing Test HAS_NO_CLASS_MEMACCESS
-- Performing Test HAS_NO_CLASS_MEMACCESS - Success
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Performing Test LMFIT_LINKS_OK
-- Performing Test LMFIT_LINKS_OK - Success
CMake Warning (dev) at /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:438 (message):
  The package name passed to `find_package_handle_standard_args` (lmfit) does
  not match the name of the calling package (Lmfit).  This can lead to
  problems in calling code that expects `find_package` result variables
  (e.g., `_FOUND`) to follow a certain pattern.
Call Stack (most recent call first):
  cmake/FindLmfit.cmake:84 (find_package_handle_standard_args)
  cmake/gmxManageLmfit.cmake:77 (find_package)
  src/gromacs/CMakeLists.txt:333 (gmx_manage_lmfit)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Found lmfit: /usr/include/include (found version "9.0.0") 
-- <<< Gentoo configuration >>>
Build type      RelWithDebInfo
Install path    /usr
Compiler flags:
C               -pipe -march=native -fno-diagnostics-color -O2
C++             -pipe -march=native -fno-diagnostics-color -O2
Linker flags:
Executable        -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 
Module          -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0
Shared            -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 

-- Configuring done
-- Generating done
-- Build files have been written to: /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3_float
 * Configuring for double precision
 * Source directory (CMAKE_USE_DIR): "/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3"
 * Build directory  (BUILD_DIR):     "/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3_double"
cmake -C /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3_double/gentoo_common_config.cmake -G Ninja -DCMAKE_INSTALL_PREFIX=/usr -DGMX_FFT_LIBRARY=fftw3 -DGMX_USE_LMFIT=EXTERNAL -DGMX_X11=no -DGMX_EXTERNAL_BLAS=no -DGMX_EXTERNAL_LAPACK=no -DGMX_OPENMP=yes -DGMX_COOL_QUOTES=yes -DGMX_USE_TNG=yes -DGMX_BUILD_MANUAL=no -DGMX_HWLOC=yes -DGMX_DEFAULT_SUFFIX=off -DGMX_SIMD=AVX2_256 -DGMX_VMD_PLUGIN_PATH=/usr/lib/vmd/plugins/*/molfile/ -DBUILD_TESTING=no -DGMX_BUILD_UNITTESTS=no -DPYTHON_EXECUTABLE=/usr/bin/python3.9 -DGMX_DOUBLE=ON -DGMX_MPI=OFF -DGMX_THREAD_MPI=yes -DGMXAPI=yes -DGMX_INSTALL_LEGACY_API=yes -DGMX_GPU=OFF  -DGMX_BINARY_SUFFIX=_d -DGMX_LIBS_SUFFIX=_d -DGMX_PYTHON_PACKAGE=no -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCMAKE_TOOLCHAIN_FILE=/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3_double/gentoo_toolchain.cmake  /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3
loading initial cache file /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3_double/gentoo_common_config.cmake
-- The C compiler identification is GNU 11.2.0
-- The CXX compiler identification is GNU 11.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/x86_64-gentoo-linux-musl-gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/x86_64-gentoo-linux-musl-g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found Python3: /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/temp/python3.9/bin/python3 (found suitable version "3.9.9", minimum required is "3.6") found components: Interpreter 
-- Found OpenMP_C: -fopenmp (found version "4.5") 
-- Found OpenMP_CXX: -fopenmp (found version "4.5") 
-- Found OpenMP: TRUE (found version "4.5")  
-- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS
-- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS
-- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - not found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - not found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - found
-- Using manually set binary suffix: "_d"
-- Using manually set library suffix: "_d"
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version: 
-- Found HWLOC: /usr/lib/libhwloc.so (found suitable version "2.5.0", minimum required is "1.5") 
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE  
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Performing Test TEST_ATOMICS
-- Performing Test TEST_ATOMICS - Success
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - supported
-- Detected build CPU vendor - AMD
-- Detected build CPU brand - AMD Ryzen 9 5950X 16-Core Processor
-- Detected build CPU family - 25
-- Detected build CPU model - 33
-- Detected build CPU stepping - 0
-- Detected build CPU features - aes amd apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf misalignsse mmx msr nonstop_tsc pclmuldq pdpe1gb popcnt pse rdrnd rdtscp sha sse2 sse3 sse4a sse4.1 sse4.2 ssse3
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for system XDR support
-- Checking for system XDR support - not present
-- Performing Test C_mavx2_mfma_FLAG_ACCEPTED
-- Performing Test C_mavx2_mfma_FLAG_ACCEPTED - Success
-- Performing Test C_mavx2_mfma_COMPILE_WORKS
-- Performing Test C_mavx2_mfma_COMPILE_WORKS - Success
-- Performing Test CXX_mavx2_mfma_FLAG_ACCEPTED
-- Performing Test CXX_mavx2_mfma_FLAG_ACCEPTED - Success
-- Performing Test CXX_mavx2_mfma_COMPILE_WORKS
-- Performing Test CXX_mavx2_mfma_COMPILE_WORKS - Success
-- Enabling 256-bit AVX2 SIMD instructions using CXX flags:  -mavx2 -mfma
-- Detecting flags to enable runtime detection of AVX-512 units on newer CPUs
-- Performing Test C_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED
-- Performing Test C_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED - Failed
-- Performing Test C_xCORE_AVX512_FLAG_ACCEPTED
-- Performing Test C_xCORE_AVX512_FLAG_ACCEPTED - Failed
-- Performing Test C_mavx512f_mfma_FLAG_ACCEPTED
-- Performing Test C_mavx512f_mfma_FLAG_ACCEPTED - Success
-- Performing Test C_mavx512f_mfma_COMPILE_WORKS
-- Performing Test C_mavx512f_mfma_COMPILE_WORKS - Success
-- Performing Test CXX_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED
-- Performing Test CXX_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED - Failed
-- Performing Test CXX_xCORE_AVX512_FLAG_ACCEPTED
-- Performing Test CXX_xCORE_AVX512_FLAG_ACCEPTED - Failed
-- Performing Test CXX_mavx512f_mfma_FLAG_ACCEPTED
-- Performing Test CXX_mavx512f_mfma_FLAG_ACCEPTED - Success
-- Performing Test CXX_mavx512f_mfma_COMPILE_WORKS
-- Performing Test CXX_mavx512f_mfma_COMPILE_WORKS - Success
-- Detecting flags to enable runtime detection of AVX-512 units on newer CPUs -  -mavx512f -mfma
-- Performing Test _Wno_unused_command_line_argument_FLAG_ACCEPTED
-- Performing Test _Wno_unused_command_line_argument_FLAG_ACCEPTED - Success
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_ 
-- Performing Test _callconv_  - Success
-- Checking for module 'fftw3'
--   Found fftw3, version 3.3.10
-- Looking for fftw_plan_many_dft in /usr/lib/libfftw3.so
-- Looking for fftw_plan_many_dft in /usr/lib/libfftw3.so - found
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/libfftw3.so
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/libfftw3.so - found
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/libfftw3.so
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/libfftw3.so - found
-- Looking for fftw_have_simd_sse in /usr/lib/libfftw3.so
-- Looking for fftw_have_simd_sse in /usr/lib/libfftw3.so - not found
-- Looking for fftw_have_sse in /usr/lib/libfftw3.so
-- Looking for fftw_have_sse in /usr/lib/libfftw3.so - not found
-- Looking for fftw_have_simd_sse2 in /usr/lib/libfftw3.so
-- Looking for fftw_have_simd_sse2 in /usr/lib/libfftw3.so - found
-- Using external FFT library - FFTW3
-- Could not convert sample image, ImageMagick convert can not be used. A possible way to fix it can be found here: https://alexvanderbist.com/2018/fixing-imagick-error-unauthorized
-- Found Sphinx: /usr/bin/sphinx-build (found suitable version "4.2.0", minimum required is "1.6.1") found components: pygments 
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- Performing Test HAS_NO_REDUNDANT_MOVE
-- Performing Test HAS_NO_REDUNDANT_MOVE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_MISSING_DECLARATIONS
-- Performing Test HAS_NO_MISSING_DECLARATIONS - Success
-- Performing Test HAS_NO_NULL_CONVERSIONS
-- Performing Test HAS_NO_NULL_CONVERSIONS - Success
-- Performing Test HAS_NO_CLASS_MEMACCESS
-- Performing Test HAS_NO_CLASS_MEMACCESS - Success
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Performing Test LMFIT_LINKS_OK
-- Performing Test LMFIT_LINKS_OK - Success
CMake Warning (dev) at /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:438 (message):
  The package name passed to `find_package_handle_standard_args` (lmfit) does
  not match the name of the calling package (Lmfit).  This can lead to
  problems in calling code that expects `find_package` result variables
  (e.g., `_FOUND`) to follow a certain pattern.
Call Stack (most recent call first):
  cmake/FindLmfit.cmake:84 (find_package_handle_standard_args)
  cmake/gmxManageLmfit.cmake:77 (find_package)
  src/gromacs/CMakeLists.txt:333 (gmx_manage_lmfit)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Found lmfit: /usr/include/include (found version "9.0.0") 
-- <<< Gentoo configuration >>>
Build type      RelWithDebInfo
Install path    /usr
Compiler flags:
C               -pipe -march=native -fno-diagnostics-color -O2
C++             -pipe -march=native -fno-diagnostics-color -O2
Linker flags:
Executable        -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 
Module          -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0
Shared            -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 

-- Configuring done
-- Generating done
-- Build files have been written to: /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3_double
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3 ...
 * Compiling for float precision
 * Source directory (CMAKE_USE_DIR): "/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3"
 * Build directory  (BUILD_DIR):     "/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3_float"
ninja -v -j4 -l0
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[300/1119] /usr/bin/x86_64-gentoo-linux-musl-gcc -DGMX_DOUBLE=0 -Isrc -I/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src -I/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/tng_io/include -Itng/include -I/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/tng_io/external/zlib -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external  -pipe -march=native -fno-diagnostics-color -O2 -fPIC -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -MF src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o.d -o src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/tng_io/src/compression/xtc2.c
[301/1119] /usr/bin/x86_64-gentoo-linux-musl-gcc -DGMX_DOUBLE=0 -Isrc -I/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src -I/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/tng_io/include -Itng/include -I/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/tng_io/external/zlib -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external  -pipe -march=native -fno-diagnostics-color -O2 -fPIC -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -MF src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o.d -o src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/tng_io/src/compression/tng_compress.c
[302/1119] /usr/bin/x86_64-gentoo-linux-musl-gcc -DGMX_DOUBLE=0 -Isrc -I/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src -I/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/tng_io/include -Itng/include -I/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/tng_io/external/zlib -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external  -pipe -march=native -fno-diagnostics-color -O2 -fPIC -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/tng_io/src/lib/md5.c
[303/1119] /usr/bin/x86_64-gentoo-linux-musl-gcc -DGMX_DOUBLE=0 -Isrc -I/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src -I/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/tng_io/include -Itng/include -I/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/tng_io/external/zlib -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external  -pipe -march=native -fno-diagnostics-color -O2 -fPIC -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/tng_io/src/compression/xtc3.c
[304/1119] cd /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3.9 -D HAVE_FULL_FUNCTIONING_PYTHON=Python3_Interpreter_FOUND -D PROJECT_VERSION=2021.3 -D PROJECT_SOURCE_DIR=/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3 -D DIRECTORIES_TO_CHECKSUM=src:python_packaging -D VERSION_CMAKEIN=/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3_float/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3_float/VersionInfo.cmake -D VERSION_STRING_OF_FORK= -D SOURCE_IS_SOURCE_DISTRIBUTION=ON -P /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/cmake/gmxGenerateVersionInfoWithoutGit.cmake
[305/1119] /usr/bin/x86_64-gentoo-linux-musl-gcc -DGMX_DOUBLE=0 -DUSE_STD_INTTYPES_H -Isrc -I/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src -I/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/tng_io/include -Itng/include -I/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/tng_io/external/zlib -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external  -pipe -march=native -fno-diagnostics-color -O2 -fPIC -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/tng_io/src/lib/tng_io.c
[306/1119] cd /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3_float/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3_float/VersionInfo.cmake -D VERSION_CMAKEIN=/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI=10.5281/zenodo.5053201 -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/cmake/gmxConfigureVersionInfo.cmake && /usr/bin/cmake -E touch utility/baseversion-gen.cpp
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[439/1119] /usr/bin/x86_64-gentoo-linux-musl-g++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -Isrc -I/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/thread_mpi/include -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/tng_io/include -isystem tng/include -isystem /usr/include/include  -pipe -march=native -fno-diagnostics-color -O2 -fPIC -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -MF src/gromacs/CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o.d -o src/gromacs/CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/gromacs/mdrun/runner.cpp
[440/1119] /usr/bin/x86_64-gentoo-linux-musl-g++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -Isrc -I/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/thread_mpi/include -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/tng_io/include -isystem tng/include -isystem /usr/include/include  -pipe -march=native -fno-diagnostics-color -O2 -fPIC -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o -MF src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o.d -o src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o -c /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/gromacs/applied_forces/awh/biaswriter.cpp
[441/1119] /usr/bin/x86_64-gentoo-linux-musl-g++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -Isrc -I/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/thread_mpi/include -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/tng_io/include -isystem tng/include -isystem /usr/include/include  -pipe -march=native -fno-diagnostics-color -O2 -fPIC -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o -MF src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o.d -o src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o -c /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/gromacs/applied_forces/awh/coordstate.cpp
[442/1119] /usr/bin/x86_64-gentoo-linux-musl-g++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -Isrc -I/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/thread_mpi/include -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/tng_io/include -isystem tng/include -isystem /usr/include/include  -pipe -march=native -fno-diagnostics-color -O2 -fPIC -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o -MF src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o.d -o src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o -c /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/gromacs/applied_forces/awh/correlationgrid.cpp
[443/1119] /usr/bin/x86_64-gentoo-linux-musl-g++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -Isrc -I/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/thread_mpi/include -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/tng_io/include -isystem tng/include -isystem /usr/include/include  -pipe -march=native -fno-diagnostics-color -O2 -fPIC -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o -MF src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o.d -o src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o -c /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/gromacs/applied_forces/awh/correlationhistory.cpp
[444/1119] /usr/bin/x86_64-gentoo-linux-musl-g++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -Isrc -I/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/thread_mpi/include -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/tng_io/include -isystem tng/include -isystem /usr/include/include  -pipe -march=native -fno-diagnostics-color -O2 -fPIC -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o -MF src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o.d -o src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o -c /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/gromacs/applied_forces/awh/histogramsize.cpp
FAILED: src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o 
/usr/bin/x86_64-gentoo-linux-musl-g++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -Isrc -I/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/thread_mpi/include -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/tng_io/include -isystem tng/include -isystem /usr/include/include  -pipe -march=native -fno-diagnostics-color -O2 -fPIC -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o -MF src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o.d -o src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o -c /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/gromacs/applied_forces/awh/histogramsize.cpp
In file included from /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/gromacs/applied_forces/awh/histogramsize.cpp:47:
/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/gromacs/applied_forces/awh/histogramsize.h:172:5: error: 'int64_t' does not name a type
  172 |     int64_t numUpdates_; /**< The number of updates performed since the start of the simulation. */
      |     ^~~~~~~
/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/gromacs/applied_forces/awh/histogramsize.h:60:1: note: 'int64_t' is defined in header '<cstdint>'; did you forget to '#include <cstdint>'?
   59 | #include "gromacs/math/vectypes.h"
  +++ |+#include <cstdint>
   60 | 
/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/gromacs/applied_forces/awh/histogramsize.h: In member function 'int gmx::HistogramSize::numUpdates() const':
/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/gromacs/applied_forces/awh/histogramsize.h:146:37: error: 'numUpdates_' was not declared in this scope; did you mean 'numUpdates'?
  146 |     int numUpdates() const { return numUpdates_; }
      |                                     ^~~~~~~~~~~
      |                                     numUpdates
/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/gromacs/applied_forces/awh/histogramsize.h: In member function 'void gmx::HistogramSize::incrementNumUpdates()':
/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/gromacs/applied_forces/awh/histogramsize.h:150:34: error: 'numUpdates_' was not declared in this scope; did you mean 'numUpdates'?
  150 |     void incrementNumUpdates() { numUpdates_ += 1; }
      |                                  ^~~~~~~~~~~
      |                                  numUpdates
/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/gromacs/applied_forces/awh/histogramsize.cpp: In constructor 'gmx::HistogramSize::HistogramSize(const gmx::AwhBiasParams&, double)':
/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/gromacs/applied_forces/awh/histogramsize.cpp:68:5: error: class 'gmx::HistogramSize' does not have any field named 'numUpdates_'
   68 |     numUpdates_(0),
      |     ^~~~~~~~~~~
/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/gromacs/applied_forces/awh/histogramsize.cpp: In member function 'void gmx::HistogramSize::restoreFromHistory(const gmx::AwhBiasStateHistory&)':
/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/gromacs/applied_forces/awh/histogramsize.cpp:270:5: error: 'numUpdates_' was not declared in this scope; did you mean 'numUpdates'?
  270 |     numUpdates_               = stateHistory.numUpdates;
      |     ^~~~~~~~~~~
      |     numUpdates
/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/gromacs/applied_forces/awh/histogramsize.cpp: In member function 'void gmx::HistogramSize::storeState(gmx::AwhBiasStateHistory*) const':
/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/gromacs/applied_forces/awh/histogramsize.cpp:281:46: error: 'numUpdates_' was not declared in this scope; did you mean 'numUpdates'?
  281 |     stateHistory->numUpdates               = numUpdates_;
      |                                              ^~~~~~~~~~~
      |                                              numUpdates
[445/1119] /usr/bin/x86_64-gentoo-linux-musl-g++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -Isrc -I/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/thread_mpi/include -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/tng_io/include -isystem tng/include -isystem /usr/include/include  -pipe -march=native -fno-diagnostics-color -O2 -fPIC -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o -MF src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o.d -o src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o -c /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/gromacs/applied_forces/awh/correlationtensor.cpp
[446/1119] /usr/bin/x86_64-gentoo-linux-musl-g++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -Isrc -I/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/thread_mpi/include -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/tng_io/include -isystem tng/include -isystem /usr/include/include  -pipe -march=native -fno-diagnostics-color -O2 -fPIC -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o -MF src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o.d -o src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o -c /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/gromacs/applied_forces/awh/pointstate.cpp
[447/1119] /usr/bin/x86_64-gentoo-linux-musl-g++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -Isrc -I/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/thread_mpi/include -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/external/tng_io/include -isystem tng/include -isystem /usr/include/include  -pipe -march=native -fno-diagnostics-color -O2 -fPIC -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o -MF src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o.d -o src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o -c /var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3/src/gromacs/applied_forces/awh/biasstate.cpp
ninja: build stopped: subcommand failed.
 * ERROR: sci-chemistry/gromacs-2021.3-r1::gentoo failed (compile phase):
 *   ninja -v -j4 -l0 failed
 * 
 * Call stack:
 *     ebuild.sh, line  127:  Called src_compile
 *   environment, line 3768:  Called cmake_src_compile
 *   environment, line 1466:  Called cmake_build
 *   environment, line 1435:  Called eninja
 *   environment, line 2376:  Called die
 * The specific snippet of code:
 *       "$@" || die "${nonfatal_args[@]}" "${*} failed"
 * 
 * If you need support, post the output of `emerge --info '=sci-chemistry/gromacs-2021.3-r1::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-chemistry/gromacs-2021.3-r1::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-chemistry:gromacs-2021.3-r1:20211209-224150.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3_float'
 * S: '/var/tmp/portage/sci-chemistry/gromacs-2021.3-r1/work/gromacs-2021.3'